IntClust (version 0.1.0)

WonM: Weighting on membership

Description

Weighting on Membership (WonM) is similar to CEC as the dendrograms are divided into clusters for a range of values for the number of clustes. However, instead of weighting the sum of the incidences matrices, the final matrix for clustering is the normal sum of all incidence matrices.

Usage

WonM(List, type = c("data", "dist", "clusters"), distmeasure = c("tanimoto",
  "tanimoto"), normalize = c(FALSE, FALSE), method = c(NULL, NULL),
  nrclusters = seq(5, 25, 1), clust = "agnes", linkage = c("flexible",
  "flexible"), alpha = 0.625)

Arguments

List

A list of data matrices. It is assumed the rows are corresponding with the objects.

type

indicates whether the provided matrices in "List" are either data matrices, distance matrices or clustering results obtained from the data. If type="dist" the calculation of the distance matrices is skipped and if type="clusters" the single source clustering is skipped. Type should be one of "data", "dist" or"clusters".

distmeasure

A vector of the distance measures to be used on each data matrix. Should be one of "tanimoto", "euclidean", "jaccard", "hamming". Defaults to c("tanimoto","tanimoto").

normalize

Logical. Indicates whether to normalize the distance matrices or not, defaults to c(FALSE, FALSE) for two data sets. This is recommended if different distance types are used. More details on normalization in Normalization.

method

A method of normalization. Should be one of "Quantile","Fisher-Yates", "standardize","Range" or any of the first letters of these names. Default is c(NULL,NULL) for two data sets.

nrclusters

A sequence of numbers of clusters to cut the dendrogram in. Defaults is a sequence of 5 to 25.

clust

Choice of clustering function (character). Defaults to "agnes".

linkage

Choice of inter group dissimilarity (character) for each data set. Defaults to c("flexible", "flexible") for two data sets.

alpha

The parameter alpha to be used in the "flexible" linkage of the agnes function. Defaults to 0.625 and is only used if the linkage is set to "flexible"

Value

The returned value is a list of two elements:

DistM

The resulting incidence matrix

Clust

The resulting clusters

The value has class 'WonM'.

Examples

# NOT RUN {
data(fingerprintMat)
data(targetMat)
L=list(fingerprintMat,targetMat)

MCF7_WonM=WonM(List=L,type="data",distmeasure=c("tanimoto", "tanimoto"),
normalize=c(FALSE,FALSE),method=c(NULL,NULL),nrclusters=seq(5,25,1),
clust="agnes",linkage=c("flexible","flexible"),alpha=0.625)
# }